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Adjustments to NEON sample tools
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- Made the sampleCode the default identifiers that is used to open tbe NEON Sample Viewer, whenever it's available for the same
- Activate and adjust SQL statements used to categorize IGSN mapping issues
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@egbot
egbot committed May 3, 2022
1 parent f8b93a6 commit 4784463
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Showing 2 changed files with 16 additions and 24 deletions.
39 changes: 16 additions & 23 deletions classes/OccurrenceSesar.php
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Original file line number Diff line number Diff line change
Expand Up @@ -544,7 +544,7 @@ public function verifySesarGuids(){
$rs->free();
}
if(isset($sesarResultArr['missing'])) $this->setMissingSesarMeta($sesarResultArr);
//$this->setSynchronizationStatus();
$this->setSynchronizationStatus();
return $sesarResultArr;
}

Expand Down Expand Up @@ -617,7 +617,7 @@ private function setMissingSesarMeta(&$sesarResultArr){
if(preg_match('/[A-Z.\s]+(\{.+)/i', $retStr, $m1)) $retStr = $m1[1];
}
$igsnObj = json_decode($retStr);
if(preg_match('/^(.+)\s*\[\s*(\d+)\s*\]$/', $igsnObj->name,$m2)){
if(preg_match('/^(.*)\s*\[\s*(\d+)\s*\]$/', $igsnObj->name,$m2)){
$catNum = $m2[1];
$occid = $m2[2];
$sesarResultArr['missing'][$lostIGSN] = array('catNum'=>$catNum,'occid'=>$occid);
Expand All @@ -634,27 +634,18 @@ private function setMissingSesarMeta(&$sesarResultArr){
private function setSynchronizationStatus(){
$status = false;
$sqlArr = array();
$sqlArr[] = 'UPDATE igsnverification SET syncStatus = "OK" WHERE occid IS NOT NULL AND catalogNumber IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN omoccurrences o ON i.occid = o.occid '.
'SET i.syncStatus = "secondaryIGSN assigned" '.
'WHERE i.catalognumber IS NOT NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN omoccuridentifiers i2 ON i.catalogNumber = i2.identifiervalue '.
'INNER JOIN omoccurrences o ON i2.occid = o.occid '.
'SET i.syncStatus = "secondaryIGSN assigned", i.occid = o.occid '.
'WHERE i.catalognumber IS NOT NULL AND i.occid IS NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN NeonSample s ON i.catalogNumber = s.sampleID '.
'INNER JOIN omoccurrences o ON s.occid = o.occid '.
'SET i.syncStatus = "secondaryIGSN assigned", i.occid = o.occid '.
'WHERE i.catalognumber IS NOT NULL AND i.occid IS NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN NeonSample s ON i.catalogNumber = s.sampleID '.
'INNER JOIN omoccurrences o ON s.occid = o.occid '.
'SET i.syncStatus = "secondaryIGSN assigned", i.occid = o.occid '.
'WHERE i.catalognumber IS NOT NULL AND i.occid IS NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN NeonSample s ON i.catalogNumber = s.alternativeSampleID '.
'INNER JOIN omoccurrences o ON s.occid = o.occid '.
'SET i.syncStatus = "secondaryIGSN assigned", i.occid = o.occid '.
'WHERE i.catalognumber IS NOT NULL AND i.occid IS NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification SET syncStatus = "" WHERE syncStatus IS NULL AND occid IS NULL AND catalogNumber IS NOT NULL';
$sqlArr[] = 'UPDATE omoccurrences o LEFT JOIN igsnverification v ON o.occurrenceid = v.igsn
SET v.syncStatus = "IGSN in portal, not in SESAR system"
WHERE o.occurrenceID LIKE "NEON%" AND v.igsn IS NULL';
$sqlArr[] = 'UPDATE igsnverification SET syncStatus = "OK" WHERE occidInPortal IS NOT NULL AND catalogNumber IS NULL';
$sqlArr[] = 'UPDATE igsnverification i INNER JOIN omoccurrences o ON i.occidInSesar = o.occid
SET i.syncStatus = "newIGSN re-assigned to same occurrence record"
WHERE i.occidInPortal IS NULL AND i.igsn != o.occurrenceID AND i.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification v INNER JOIN omoccuridentifiers i ON v.catalogNumber = i.identifierValue
INNER JOIN omoccurrences o ON i.occid = o.occid
SET v.syncStatus = "newIGSN, new record, matching NEON ID"
WHERE v.occidInPortal IS NULL AND v.igsn != o.occurrenceID AND v.syncStatus IS NULL';
$sqlArr[] = 'UPDATE igsnverification SET syncStatus = "Occurrence not in portal" WHERE occidInPortal IS NULL AND catalogNumber IS NOT NULL AND syncStatus IS NULL';
foreach($sqlArr as $sql){
if(!$this->conn->query($sql)){
$errorStr = 'ERROR setting syncStatus: '.$this->conn->error;
Expand Down Expand Up @@ -731,6 +722,8 @@ public function syncIGSN($occid,$catalogNumber,$igsn){
private function getSesarApiData($url, $method = 'get', $requestData = null){
$retArr = array();
$ch = curl_init();
curl_setopt($ch, CURLOPT_SSL_VERIFYPEER, 0);
curl_setopt($ch, CURLOPT_SSL_VERIFYHOST, 0);
curl_setopt($ch, CURLOPT_URL, $url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch, CURLOPT_HTTPHEADER, array ( 'Accept: application/json' ));
Expand Down
1 change: 0 additions & 1 deletion collections/individual/index.php
View file
Original file line number Diff line number Diff line change
Expand Up @@ -970,7 +970,6 @@ function initializeMap(){
$displayStr = $idArr[0];
if($idKey == 'NEON sampleCode (barcode)') $iUrl = str_replace('sampleTag','barcode',$iUrl);
$indUrl = str_replace('--OTHERCATALOGNUMBERS--',$idArr[0],$iUrl);
if($idKey == 'NEON sampleID') break;
if($idKey == 'NEON sampleCode (barcode)') break;
}
}
Expand Down

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